Statistical Field Theory for Polar Fluids Bilin Zhuang, and Zhen-Gang Wang

Total Page:16

File Type:pdf, Size:1020Kb

Statistical Field Theory for Polar Fluids Bilin Zhuang, and Zhen-Gang Wang Statistical field theory for polar fluids Bilin Zhuang, and Zhen-Gang Wang Citation: The Journal of Chemical Physics 149, 124108 (2018); doi: 10.1063/1.5046511 View online: https://doi.org/10.1063/1.5046511 View Table of Contents: http://aip.scitation.org/toc/jcp/149/12 Published by the American Institute of Physics THE JOURNAL OF CHEMICAL PHYSICS 149, 124108 (2018) Statistical field theory for polar fluids Bilin Zhuang1,2 and Zhen-Gang Wang1,a) 1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA 2Department of Materials Science and Engineering, Institute of High Performance Computing, Singapore 138632, Singapore (Received 28 June 2018; accepted 3 September 2018; published online 26 September 2018) Using a variational field-theoretic approach, we derive a theory for polar fluids. The theory naturally accounts for the reaction field without resorting to the cavity construct and leads to a simple formula for the dielectric constant in terms of the molecular dipole moment and density. We apply our formula to calculate the dielectric constants of nonpolarizable liquid models for more than a hundred small molecules without using any adjustable parameters. Our formula predicts dielectric constants of these nonpolarizable liquid models more accurately than the Onsager theory and previous field-theoretic dielectric theories, as demonstrated by the closer agreement to the simulation results. The general theory also yields the free energy, which can describe the response of polar fluids under applied electric fields. Published by AIP Publishing. https://doi.org/10.1063/1.5046511 I. INTRODUCTION detailed information about the molecular interaction is often unavailable.17,20 Since then, more sophisticated theories for The dielectric constant is one of the most basic properties the dielectric constant have been developed based on per- of fluids. It is fundamental to many aspects of science and turbative expansions,21–23 cluster expansions,24–28 integral- technology, including behaviors of biological molecules,1,2 equation theories,29–34 and by considering the specific shapes mechanisms of chemical reactions,3–5 fabrication of new mate- of molecules35,36 or intermolecular bonding.37 However, the rials,6–8 solubility of polar and nonpolar species,9,10 and devel- Debye equation and the Onsager equation remain popular due opment of energy storage devices.11 Accurate determination of to their simplicity. the dielectric constant from molecular parameters, especially Despite the many attempts, there remains a need for a sim- in the liquid phase, remains a challenge, whether theoretically ple theory for calculating dielectric constants of fluids based or through computer simulations.11 on readily available molecular parameters. Methods based on Many attempts have been made.12,13 In 1912, Debye perturbative expansions are unsatisfactory because the series derived an equation relating the dielectric constant to the often do not converge with increasing number of terms.38 molecular permanent dipole moment and the isotropic polar- Cluster expansion methods and integral-equation methods are izability. As Debye assumed each dipole independently inter- able to relate dielectric constants to molecular properties, but acts with the applied field, his theory did not take into the required five-dimensional correlation functions (three for account the intermolecular dipole-dipole correlations; there- positions and two for orientations) are very cumbersome to fore, the Debye theory is only applicable for gas-phase sys- evaluate.28,39 tems in the dilute limit.14,15 In 1936, Onsager developed In recent years, progress in field-theoretic statistical- a theory by considering a point dipole in a cavity that is mechanical methods has provided an avenue for the embedded in a homogeneous dielectric continuum. This point development of new and simple expressions for dielectric dipole induces polarization in the surrounding medium, which constants. An additional important advantage of the field- gives rise to a reaction field that in turn influences the theoretic approach is that it can be conveniently integrated into dipole alignment in the cavity.16 The Onsager theory yields a wide range of platforms for studying soft-matter and poly- a much improved prediction for liquid dielectric constants meric systems where the molecules are modeled with the same than the Debye theory, as validated by experimental mea- approach.40–42 One of the simpler field-theoretic methods is surements.17 Shortly after, Kirkwood extended Onsager’s the- the self-consistent-field theory (SCFT), where one approxi- ory by introducing a g-factor to account for the short-range mates the partition function using the saddle-point approxi- orientational correlation between the molecules.18 While mation. Several studies have applied this approach43–47 and Kirkwood’s formulation is especially relevant for determin- the results are comparable to the predictions of the Debye the- ing dielectric constants with computer simulation,19 it is ory. Beyond the saddle-point approximation, Levy, Andelman, often difficult to evaluate the g-factor analytically because and Orland derived an expression for the dielectric constant by considering the one-loop expansion of the free energy.48,49 More recently, Martin et al. derived the dielectric constant a)[email protected] by pursuing a simple gaussian field approximation to the 0021-9606/2018/149(12)/124108/13/$30.00 149, 124108-1 Published by AIP Publishing. 124108-2 B. Zhuang and Z.-G. Wang J. Chem. Phys. 149, 124108 (2018) field-theoretic Hamiltonian.50 However, the numerical per- molecule has a permanent dipole moment of magnitudeµ ¯. formance of the predictions by these field-theoretic theories The microscopic state of the system can be specified by the is less than satisfactory when compared to the simulation or set of positions and dipole vectors of all molecules f(ri, µi): experimental data. In this work, we develop a field-theoretic i = 1, 2, :::, Ng, where ri and µi denote, respectively, the posi- theory for calculating dielectric constants of pure liquids using tion and the dipole vector (where jµi j = µ¯) of the ith molecule. a variational approach,51,52 with the goal to improve the over- The electrostatic interaction energy U of the system is the sum all accuracy in predicting dielectric constants using only a few of all pairwise dipole-dipole interactions and the interaction readily available parameters. energy with the applied field, The dipolar renormalized gaussian fluctuation (DRGF) N N N theory presented in this work is formulated using a field-based 1 X X X U = µ T(r − r )µ − µ · E (r ), (1) gaussian reference action that involves an interaction tensor 2 i i j j i 0 i i=1 j=1 i=1 and the average of the fluctuating field as the variational param- i,j eters. The self-consistency condition on the interaction tensor and the average field naturally accounts for the effects of the where T(r) = −∇∇(1/4π"0|r|) is the dipole-dipole interaction reaction field. While in the current work we consider nonpo- tensor, with "0 being the vacuum permittivity. larizable fluids for simplicity, effects of polarizability can be Mathematically, improper integrals involving T(r) are included in a straightforward way and we reserve the effort nonunique and lead to a problem of “conditional convergence.” 54,55 for an upcoming paper. The resulting theory consists of sim- However, the problem is well understood and a consistent ple analytical expressions for the free energy and the dielectric interpretation is obtained by representing T(r) in the following 56 constant. In particular, the dielectric constant of a liquid can form: be calculated based on the permanent dipole moment and the 1 1 number concentration of the molecules, both being readily T(r) = −H(jrj − η)rr + 1δ(r) 4π"0jrj 3"0 available parameters for many systems, without the need for ! 1 3rr 1 any fitting parameters. We apply the DRGF theory to calculate = H(jrj − η) 1 − + 1δ(r), (2) 3 2 the dielectric constants of nonpolarizable molecular models 4π"0jrj " jrj # 3"0 of a wide range of liquids, and we find the results from the where 1 is the unit dyadic, δ(r) is the Dirac delta function, DRGF theory provide better agreement with simulation data and H(x) is the Heaviside step function. η is a regularization than previous field-theoretic approaches.43–50 The line of best- parameter which will eventually be taken to be 0 in the final fit through our predicted dielectric constants vs. simulation calculations. Since both terms in T(r) are well defined, it is data has a slope very close to 1 on a log-log plot, which is now straightforward to compute the Fourier transform of T(r) better than the Onsager theory. and the result is39,56 The rest of this article is organized as follows. In Sec.II, we describe the model and formulate the exact partition func- kk T(k) = , (3) 2 tion of the system in the field-theoretic representation. Then, "0k we introduce a gaussian reference action and apply the vari- H ational approach based on the Gibbs-Feynman-Bogoliubov where a tilde above a quantity denotes the Fourier trans- ˜ −ik·r 2 variational principle to derive a general theory for the free form f (k) = s dr f (r)e . Noting that kk/k is a projection energy of dipolar liquids. We then consider a weak applied operator, we have the following relation: field in the linear response regime to obtain an expression n " T(k) = " T(k), (4) for the dielectric constant of a liquid. In Sec. III, we apply 0 0 our theory to calculate the dielectric constants for the GAFF which turns out to be usefulH in the algebraicH manipulations. In (generalized Amber force field) and the OPLS/AA (all-atom addition, T(k = 0) = 1=3"0 follows from Eq.
Recommended publications
  • Development of an Advanced Force Field for Water Using Variational Energy Decomposition Analysis Arxiv:1905.07816V3 [Physics.Ch
    Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis Akshaya K. Das,y Lars Urban,y Itai Leven,y Matthias Loipersberger,y Abdulrahman Aldossary,y Martin Head-Gordon,y and Teresa Head-Gordon∗,z y Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley CA 94720 z Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, University of California, Berkeley CA 94720 E-mail: [email protected] Abstract Given the piecewise approach to modeling intermolecular interactions for force fields, they can be difficult to parameterize since they are fit to data like total en- ergies that only indirectly connect to their separable functional forms. Furthermore, by neglecting certain types of molecular interactions such as charge penetration and charge transfer, most classical force fields must rely on, but do not always demon- arXiv:1905.07816v3 [physics.chem-ph] 27 Jul 2019 strate, how cancellation of errors occurs among the remaining molecular interactions accounted for such as exchange repulsion, electrostatics, and polarization. In this work we present the first generation of the (many-body) MB-UCB force field that explicitly accounts for the decomposed molecular interactions commensurate with a variational energy decomposition analysis, including charge transfer, with force field design choices 1 that reduce the computational expense of the MB-UCB potential while remaining accu- rate. We optimize parameters using only single water molecule and water cluster data up through pentamers, with no fitting to condensed phase data, and we demonstrate that high accuracy is maintained when the force field is subsequently validated against conformational energies of larger water cluster data sets, radial distribution functions of the liquid phase, and the temperature dependence of thermodynamic and transport water properties.
    [Show full text]
  • FORCE FIELDS for PROTEIN SIMULATIONS by JAY W. PONDER
    FORCE FIELDS FOR PROTEIN SIMULATIONS By JAY W. PONDER* AND DAVIDA. CASEt *Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 51. Louis, Missouri 63110, and tDepartment of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 I. Introduction. ...... .... ... .. ... .... .. .. ........ .. .... .... ........ ........ ..... .... 27 II. Protein Force Fields, 1980 to the Present.............................................. 30 A. The Am.ber Force Fields.............................................................. 30 B. The CHARMM Force Fields ..., ......... 35 C. The OPLS Force Fields............................................................... 38 D. Other Protein Force Fields ....... 39 E. Comparisons Am.ong Protein Force Fields ,... 41 III. Beyond Fixed Atomic Point-Charge Electrostatics.................................... 45 A. Limitations of Fixed Atomic Point-Charges ........ 46 B. Flexible Models for Static Charge Distributions.................................. 48 C. Including Environmental Effects via Polarization................................ 50 D. Consistent Treatment of Electrostatics............................................. 52 E. Current Status of Polarizable Force Fields........................................ 57 IV. Modeling the Solvent Environment .... 62 A. Explicit Water Models ....... 62 B. Continuum Solvent Models.......................................................... 64 C. Molecular Dynamics Simulations with the Generalized Born Model........
    [Show full text]
  • Force Fields for MD Simulations
    Force Fields for MD simulations • Topology/parameter files • Where do the numbers an MD code uses come from? • How to make topology files for ligands, cofactors, special amino acids, … • How to obtain/develop missing parameters. • QM and QM/MM force fields/potential energy descriptions used for molecular simulations. The Potential Energy Function Ubond = oscillations about the equilibrium bond length Uangle = oscillations of 3 atoms about an equilibrium bond angle Udihedral = torsional rotation of 4 atoms about a central bond Unonbond = non-bonded energy terms (electrostatics and Lenard-Jones) Energy Terms Described in the CHARMm Force Field Bond Angle Dihedral Improper Classical Molecular Dynamics r(t +!t) = r(t) + v(t)!t v(t +!t) = v(t) + a(t)!t a(t) = F(t)/ m d F = ! U (r) dr Classical Molecular Dynamics 12 6 &, R ) , R ) # U (r) = . $* min,ij ' - 2* min,ij ' ! 1 qiq j ij * ' * ' U (r) = $ rij rij ! %+ ( + ( " 4!"0 rij Coulomb interaction van der Waals interaction Classical Molecular Dynamics Classical Molecular Dynamics Bond definitions, atom types, atom names, parameters, …. What is a Force Field? In molecular dynamics a molecule is described as a series of charged points (atoms) linked by springs (bonds). To describe the time evolution of bond lengths, bond angles and torsions, also the non-bonding van der Waals and elecrostatic interactions between atoms, one uses a force field. The force field is a collection of equations and associated constants designed to reproduce molecular geometry and selected properties of tested structures. Energy Functions Ubond = oscillations about the equilibrium bond length Uangle = oscillations of 3 atoms about an equilibrium bond angle Udihedral = torsional rotation of 4 atoms about a central bond Unonbond = non-bonded energy terms (electrostatics and Lenard-Jones) Parameter optimization of the CHARMM Force Field Based on the protocol established by Alexander D.
    [Show full text]
  • FORCE FIELDS and CRYSTAL STRUCTURE PREDICTION Contents
    FORCE FIELDS AND CRYSTAL STRUCTURE PREDICTION Bouke P. van Eijck ([email protected]) Utrecht University (Retired) Department of Crystal and Structural Chemistry Padualaan 8, 3584 CH Utrecht, The Netherlands Originally written in 2003 Update blind tests 2017 Contents 1 Introduction 2 2 Lattice Energy 2 2.1 Polarcrystals .............................. 4 2.2 ConvergenceAcceleration . 5 2.3 EnergyMinimization .......................... 6 3 Temperature effects 8 3.1 LatticeVibrations............................ 8 4 Prediction of Crystal Structures 9 4.1 Stage1:generationofpossiblestructures . .... 9 4.2 Stage2:selectionoftherightstructure(s) . ..... 11 4.3 Blindtests................................ 14 4.4 Beyondempiricalforcefields. 15 4.5 Conclusions............................... 17 4.6 Update2017............................... 17 1 1 Introduction Everybody who looks at a crystal structure marvels how Nature finds a way to pack complex molecules into space-filling patterns. The question arises: can we understand such packings without doing experiments? This is a great challenge to theoretical chemistry. Most work in this direction uses the concept of a force field. This is just the po- tential energy of a collection of atoms as a function of their coordinates. In principle, this energy can be calculated by quantumchemical methods for a free molecule; even for an entire crystal computations are beginning to be feasible. But for nearly all work a parameterized functional form for the energy is necessary. An ab initio force field is derived from the abovementioned calculations on small model systems, which can hopefully be generalized to other related substances. This is a relatively new devel- opment, and most force fields are empirical: they have been developed to reproduce observed properties as well as possible. There exists a number of more or less time- honored force fields: MM3, CHARMM, AMBER, GROMOS, OPLS, DREIDING..
    [Show full text]
  • Dynamics of Ions in a Water Drop Using the AMOEBA Polarizable Force Field Florian Thaunay, Gilles Ohanessian, Carine Clavaguera
    Dynamics of ions in a water drop using the AMOEBA polarizable force field Florian Thaunay, Gilles Ohanessian, Carine Clavaguera To cite this version: Florian Thaunay, Gilles Ohanessian, Carine Clavaguera. Dynamics of ions in a water drop using the AMOEBA polarizable force field. Chemical Physics Letters, Elsevier, 2017, 671, pp.131-137. 10.1016/j.cplett.2017.01.024. hal-01999944 HAL Id: hal-01999944 https://hal.archives-ouvertes.fr/hal-01999944 Submitted on 5 Feb 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Chemical Physics Letters 671 (2017) 131–137 Contents lists available at ScienceDirect Chemical Physics Letters journal homepage: www.elsevier.com/locate/cplett Research paper Dynamics of ions in a water drop using the AMOEBA polarizable force field ⇑ Florian Thaunay, Gilles Ohanessian, Carine Clavaguéra LCM, CNRS, Ecole Polytechnique, Université Paris Saclay, 91128 Palaiseau, France article info abstract Article history: Various ions carrying a charge from À2 to +3 were confined in a drop of 100 water molecules as a way to Received 13 October 2016 model coordination properties inside the cluster and at the interface. The behavior of the ions has been In final form 10 January 2017 followed by molecular dynamics with the AMOEBA polarizable force field.
    [Show full text]
  • Electronic Supplementary Information CHARMM All Atom Force Field
    Electronic Supplementary Information CHARMM all atom force field employs a Lennard-Jones (6-12) function to describe Van der Waals interactions. This potential is a combination of attractive and repulsive contributions. The repulsive term describes internuclear electrostatic repulsion and short-range repulsive forces (or exchange forces) between electrons with the same spin. The attractive term is due to dispersion forces, which in turn are due to instantaneous dipoles arising during the fluctuations in the electron clouds. The form of the potential energy function of two interacting atoms is: 12 6 éæs ö æs ö ù VvdW = 4e êç ÷ - ç ÷ ú ëêè r ø è r ø ûú Where r is the distance between the two atoms, s is the collision diameter (the distance at the zero energy) and e is the Lennard-Jones well depth. For a q atom and a c atom, these empirical parameters are expressed from the Lorentz-Berthelot mixing rules: 1 s = (s +s ) qc 2 qq cc e qc = e qqe cc Van der Waals interactions are also important to well describe the interaction between QM and MM regions in hybrid QM/MM enzyme simulation. The Van der Waals parameters relative to the QM atoms of the FAAH-oleamide complex, applied in all the simulations performed, are reported in the table below. These are consistent to those reported in the combined parameter file (CHARMM22 for protein, CHARMM27 for lipid) par_all27_prot_lipid.prm. For further details see www.charmm.org PRIVILEGED DOCUMENT FOR REVIEW PURPOSES ONLY ATOM NAME ATOM TYPE e (kcal mole-1) s (Å) Notes O1 O -0.120000 1.700000 Oleamide
    [Show full text]
  • Computation of Free Energy
    Helvetica Chimica Acta ± Vol. 85 (2002) 3113 Computation of Free Energy by Wilfred F. van Gunsteren*a), Xavier Daurab), and Alan E. Markc) a) Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH-Hˆnggerberg, CH-8093 Zurich (e-mail: [email protected]) b) Institucio¬ Catalana de Recerca i Estudis AvanÁats (ICREA) and Institut of Biotechnologia i de Biomedicina, Universitat Auto¡noma de Barcelona, E-08193 Bellaterra c) Department of Biophysical Chemistry, University of Groningen, NL-9747 AG Groningen Dedicated to Professor Dieter Seebach on the occasion of his 65th birthday Many quantities that are standardly used to characterize a chemical system are related to free-energy differences between particular states of the system. By statistical mechanics, free-energy differences may be expressed in terms of averages over ensembles of atomic configurations for the molecular system of interest. Here, we review the most useful formulae to calculate free-energy differences from ensembles generated by molecular simulation, illustrate a number of recent developments, and highlight practical aspects of such calculations with examples selected from the literature. 1. Introduction. ± The probability of finding a molecular system in one state or the other is determined by the difference in free energy between those two states. As a consequence, free-energy differences may be directly related to a wide range of fundamental chemical quantities such as binding constants, solubilities, partition coefficients, and adsorption coefficients. By means of statistical mechanics, free-energy differences may also be expressed in terms of averages over ensembles of atomic configurations for the molecular system of interest.
    [Show full text]
  • Behavior of Gas Reveals the Existence of Antigravity Gaseous Nature More Precisely Described by Gravity-Antigravity Forces
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 29 January 2020 Article Behavior of gas reveals the existence of antigravity Gaseous nature more precisely described by gravity-antigravity forces Chithra K. G. Piyadasa* Electrical and Computer engineering, University of Manitoba, 75, Chancellors Circle, Winnipeg, MB, R3T 5V6, Canada. * Correspondence: [email protected]; Tel.: +1 204 583 1156 Abstract: The Author’s research series has revealed the existence in nature, of gravitational repulsion force, i,e., antigravity, which is proportional to the content of thermal energy of the particle. Such existence is in addition to the gravitational attraction force, accepted for several hundred years as proportional to mass. Notwithstanding such long acceptance, gravitational attraction acting on matter has totally been neglected in thermodynamic calculations in derivation of the ideal gas law. Both the antigravity force and the gravitational force have to be accommodated in an authentic elucidation of ideal gas behavior. Based on microscopic behavior of air molecules under varying temperature, this paper presents: firstly, the derivation of the mathematical model of gravitational repulsive force in matter; secondly, mathematical remodeling of the gravitational attractive force in matter. Keywords: gravitational attraction, gravitational repulsion, antigravity, intermolecular forces, specific heat, thermal energy, adiabatic and isothermal expansion. 1. Introduction As any new scientific revelation has a bearing on the accepted existing knowledge, some analysis of the ideal gas law becomes expedient. The introduction discusses the most fundamental concepts relating to the ideal gas law and they are recalled in this introduction with fine detail to show how they contradict the observations made in this discussion.
    [Show full text]
  • Molmod: an Open Access Database of Force Fields for Molecular
    MolMod: An open access database of force fields for molecular simulations of fluids Simon Stephan,a Martin Thomas Horsch,b Jadran Vrabec,c Hans Hassea aTechnische Universit¨at Kaiserslautern, Laboratory of Engineering Thermodynamics (LTD), Erwin-Schr¨odinger-Str. 44, 67663 Kaiserslautern, Germany bUK Research and Innovation, STFC Daresbury Laboratory, Keckwick Lane, Daresbury, Cheshire WA4 4AD, United Kingdom cTechnische Universit¨at Berlin, Thermodynamics and Process Engineering, Straße des 17. Juni 135, 10623 Berlin, Germany ARTICLE HISTORY Compiled April 11, 2019 ABSTRACT The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de/ and contains presently intermolecular force fields for over 150 pure fluids. It was developed and is maintained by the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS). The set of molecular models in the MolMod database provides a coherent framework for molecular simulations of fluids. The molecular models in the MolMod database consist of Lennard-Jones interaction sites, point charges, and point dipoles and quadrupoles, which can be equivalently represented by multiple point charges. The force fields can be exported as input files for the simulation programs ms2 and ls1 mardyn, Gromacs, and LAMMPS. To characterise the semantics associated with the numerical database content, a force-field nomenclature is introduced that can also be used in other contexts in materials modelling at the atomistic and mesoscopic levels. The models of the pure substances that are included in the data base were generally optimised such arXiv:1904.05206v1 [physics.comp-ph] 9 Apr 2019 as to yield good representations of experimental data of the vapour-liquid equilibrium with a focus on the vapour pressure and the saturated liquid density.
    [Show full text]
  • Developing Protonated and Deprotonated Cysteine Side-Chain Parameters for POSSIM Force Field
    Developing Protonated and Deprotonated Cysteine Side-Chain Parameters for POSSIM Force Field A Major Qualifying Project Submitted to the Faculty of Worcester Polytechnic Institute in partial fulfillment of the requirements for the Degree in Bachelor of Science In Chemistry by Anetta Goldsher Project Advisor Professor George Kaminski This report represents work of WPI undergraduate students submitted to the faculty as evidence of a degree requirement. WPI routinely publishes these reports on its web site without editorial or peer review. For more information about the projects program at WPI, see http://www.wpi.edu/Academics/Projects. Table of Contents ACKNOWLEDGEMENTS ........................................................................................................................ 2 ABSTRACT ................................................................................................................................................ 3 1. INTRODUCTION .................................................................................................................................. 4 2. BACKGROUND ..................................................................................................................................... 6 2.1 BASICS OF COMPUTATIONAL CHEMISTRY ..................................................................................................... 6 2.2 AB INITIO ............................................................................................................................................................
    [Show full text]
  • Trypsin-Ligand Binding Affinities Calculated Using an Effective
    www.nature.com/scientificreports OPEN Trypsin-Ligand binding afnities calculated using an efective interaction entropy method under Received: 30 June 2017 Accepted: 1 December 2017 polarized force feld Published: xx xx xxxx Yalong Cong1, Mengxin Li1, Guoqiang Feng1, Yuchen Li1, Xianwei Wang2 & Lili. Duan1 Molecular dynamics (MD) simulation in the explicit water is performed to study the interaction mechanism of trypsin-ligand binding under the AMBER force feld and polarized protein-specifc charge (PPC) force feld combined the new developed highly efcient interaction entropy (IE) method for calculation of entropy change. And the detailed analysis and comparison of the results of MD simulation for two trypsin-ligand systems show that the root-mean-square deviation (RMSD) of backbone atoms, B-factor, intra-protein and protein-ligand hydrogen bonds are more stable under PPC force feld than AMBER force feld. Our results demonstrate that the IE method is superior than the traditional normal mode (Nmode) method in the calculation of entropy change and the calculated binding free energy under the PPC force feld combined with the IE method is more close to the experimental value than other three combinations (AMBER-Nmode, AMBER-IE and PPC-Nmode). And three critical hydrogen bonds between trypsin and ligand are broken under AMBER force feld. However, they are well preserved under PPC force feld. Detailed binding interactions of ligands with trypsin are further analyzed. The present work demonstrates that the polarized force feld combined the highly efcient IE method is critical in MD simulation and free energy calculation. Underlying the interaction mechanism of protein-ligand at atomic level is vital in biomolecular and can provide extremely high value in drug design.
    [Show full text]
  • 1 Force Fields
    1 Force fields 1.1 Introduction The term force field is slightly misleading, since it refers to the parameters of the potential used to calculate the forces (via gradient) in molecular dynamics simulations. The un- derlying idea is to create a certain number of atom types upon which any bonds, angles, impropers, dihedrals and long-range interactions may be described. More atomtypes than elements are necessary, since the chemical surroundings greatly influence the parameters. The angle between carbons in alkyne side chains will obviously differ from that of car- bons in a benzene ring, so two different atom types are used to describe them. Since all simultations rely greatly upon the correctness of these parameters, it is important to know, where these parameters come from and how they may be derived in case some are lacking. One of the most commonly used force fields is the OPLS (Optimized Potential for Liquid Simulations) force field, developed by William L. Jorgensen at Purdue University and later at Yale University. It shall be our main example here. 1.2 A word on AMBER The functional form of the OPLS force field is very similar to that of AMBER (Assisted Model Building and Energy Refinement), originally developed by Peter Kollman’s group at the University of California San Francisco, which has the form [1, 2]: 1 2 2 V ( ~r )= k (r r0) + k (θ θ0) { N } 2 b − θ − bondsX anglesX 1 + V [1 + cos(nω γ)] 2 n − torsions NX−1 N 12 6 σij σij qiqj + 4ǫij + + r j r j 4πǫ0r i=1 j=i+1 ( " i i # ij ) X X 1.3 Functional form of OPLS Based upon AMBER, Jorgensen et al.
    [Show full text]